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California Provides $40M for Stanford-led Stem Cell Genomics Center

NEW YORK (GenomeWeb News) – Stanford University has been awarded $40 million from the California Institute for Regenerative Medicine to work with several partners to create a center that will focus on applying genomics approaches and technologies to stem cell science.

Stanford and its collaborators will use the CIRM funding to create the Center of Excellence in Stem Cell Genomics, which will apply genomics in developing better ways to use stem cells in research and treatment, and enhance understanding about diseases like cancer, diabetes, heart disease, and mental health, Stanford said yesterday.

The other partners working with the center include the Salk Institute for Biological Studies; the J. Craig Venter Institute; the University of California Santa Cruz; UC San Diego, Scripps Research Institute; and Illumina.

"Bringing together this team to do this kind of work means we will be better able to understand how stem cells change as they grow and become different kinds of cells," CIRM President Alan Trounson said in a statement from the stem cell agency. "That deeper knowledge, [which] you can only get through a genomic analysis of the cells, will help us develop better ways of using these cells to come up with new treatments for deadly diseases."

The funding was approved yesterday by CIRM's board, the Independent Citizen's Oversight Committee, which had set aside $40 million two years ago to fund stem cell genomics initiatives and had received several proposals. Although the ICOC was free to fund more than one of these stem cell genomics projects, it ultimately decided to award all of the funds to the Stanford-led

According to CIRM, $19 million of the funding for the center will support independent and collaborative projects focused on disease mechanisms and developing new technologies.

The center will be a resource for other stem cell researchers and engage in outside collaborations, but it also will pursue its own projects, such as collecting and characterizing induced pluripotent stem cell lines, using single-cell genomics techniques to understand cellular subpopulations, and building computational tools for analyzing networks that underlie stem cell and genome function.

CIRM, also known as the California Stem Cell Agency, was created in 2004 after voters approved a proposition to provide $3 billion for stem cell research projects and programs at institutes around the state.

The Center of Excellence in Stem Cell Genomics will be led by Co-directors Michael Snyder, chair of genetics at Stanford, and Joseph Ecker, a professor in the plant biology lab at Salk.

Snyder, who also directs Stanford's Center for Genomics and Personalized Medicine, said many of the partners in the project have developed cutting-edge technologies that will be available through the center.

UC Santa Cruz will run the center's data collection and management component, which will handle the large amounts of data these stem cell genomics projects generate.

"Stem cell researchers are collecting large amounts of DNA and RNA sequence data, and data analysis is becoming a bottleneck to discovery," Josh Stuart, a professor of biomolecular engineering in UCSC's Baskin School of Engineering, said in a statement. "We will provide the high-performance infrastructure needed to manage that data."

UCSC added that Stuart will also be working with Trey Ideker at UC San Diego to develop new "machine learning" tools specific for making discoveries in the anticipated stem cell datasets.